bims-pideca 2021-07-18 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2021‒07‒18
37 papers selected by
Ralitsa Radostinova Madsen
University College London Cancer Institute

The innate immune kinase TBK1 directly increases mTORC2 activity and downstream signaling to Akt.
Akt phosphorylates insulin receptor substrate to limit PI3K-mediated PIP3 synthesis.
Thyroid Hormone Receptor Beta Inhibits PI3K-Akt-mTOR Signaling Axis in Anaplastic Thyroid Cancer via Genomic Mechanisms.
TSC2 regulates lysosome biogenesis via a non-canonical RAGC and TFEB-dependent mechanism.
An mTORC1-GRASP55 signaling axis controls unconventional secretion to reshape the extracellular proteome upon stress.
Treating Alpelisib-Induced Hyperglycemia with Very Low Carbohydrate Diets and Sodium-Glucose Co-Transporter 2 Inhibitors: A Case Series.
PI3K Promotes Basal Cell Carcinoma Growth Through Kinase-Induced p21 Degradation.
Modulation of Akt vs Stat3 activity by the focal adhesion kinase in non-neoplastic mouse fibroblasts.
Two Monogenetic Disorders, Activated PI3-Kinase-δ Syndrome 2 and Smith-Magenis Syndrome, in One Patient: Case Report and a Literature Review of Neurodevelopmental Impact in Primary Immunodeficiencies Associated With Disturbed PI3K Signaling.
Plasma Cell-Free DNA Profiling of PTEN-PI3K-AKT Pathway Aberrations in Metastatic Castration-Resistant Prostate Cancer.
Activated PI3Kinase Delta Syndrome-A Multifaceted Disease.
Morphological screening of mesenchymal mammary tumor organoids to identify drugs that reverse epithelial-mesenchymal transition.
BCG Vaccine-Associated Complications in Patients with PTEN Hamartoma Tumor Syndrome.
Microenvironmental control of cell fate decisions in mammary gland development and cancer.
Cell line-specific network models of ER+ breast cancer identify potential PI3Kα inhibitor resistance mechanisms and drug combinations.
Utility of Serial cfDNA NGS for Prospective Genomic Analysis of Patients on a Phase I Basket Study.
UCSC Cell Browser: Visualize Your Single-Cell Data.
mTORC1 activity regulates post-translational modifications of glycine decarboxylase to modulate glycine metabolism and tumorigenesis.
The effectiveness of monotherapy with PI3K/AKT/mTOR pathway inhibitors in ovarian cancer: A meta-analysis.
Functional assessment of two variants of unknown significance in TEK by endothelium-specific expression in zebrafish embryos.
Redefining the specificity of phosphoinositide-binding by human PH domain-containing proteins.
Subcutaneous adipose tissue metabolic function and insulin sensitivity in people with obesity.
Final results of the double-blind placebo-controlled randomized phase 2 LOTUS trial of first-line ipatasertib plus paclitaxel for inoperable locally advanced/metastatic triple-negative breast cancer.
Insulin Resistance in Skeletal Muscle Selectively Protects the Heart in Response to Metabolic Stress.
Ipatasertib plus abiraterone and prednisolone in metastatic castration-resistant prostate cancer (IPATential150): a multicentre, randomised, double-blind, phase 3 trial.
Translational control of stem cell function.
Multiplexed functional genomic analysis of 5' untranslated region mutations across the spectrum of prostate cancer.
Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms in cardiomyocytes.
MK2 degradation as a sensor of signal intensity that controls stress-induced cell fate.
Improved CRISPR genome editing using small highly active and specific engineered RNA-guided nucleases.
Transcription coordinates histone amounts and genome content.
Physiological impact of in vivo stable isotope tracing on cancer metabolism.
E2F/Dp inactivation in fat body cells triggers systemic metabolic changes.
Inhibition of mTOR signaling and clinical activity of metformin in oral premalignant lesions.
Role of PI3K/Akt signaling pathway in cardiac fibrosis.
FoxO3 deficiency in cortical astrocytes leads to impaired lipid metabolism and aggravated amyloid pathology.
Mitofusion is required for MOTS-c induced GLUT4 translocation.

J Biol Chem. 2021 Jul 07. pii: S0021-9258(21)00742-0. [Epub ahead of print] 100942

The innate immune kinase TBK1 directly increases mTORC2 activity and downstream signaling to Akt.

Aaron Seth Tooley, Dubek Kazyken, Cagri Bodur, Ian E Gonzalez, Diane C Fingar.

  TBK1 responds to microbes to initiate cellular responses critical for host innate immune defense. We found previously that TBK1 phosphorylates mTOR (mechanistic target of rapamycin) on S2159 to increase mTOR complex 1 (mTORC1) signaling in response to the growth factor EGF and the viral dsRNA mimetic poly(I:C). mTORC1 and the less well studied mTORC2 respond to diverse cues to control cellular metabolism, proliferation, and survival. While TBK1 has been linked to Akt phosphorylation, a direct relationship between TBK1 and mTORC2, an Akt kinase, has not been described. By studying MEFs lacking TBK1, as well as MEFs, macrophages, and mice bearing an Mtor S2159A knock-in allele (MtorA/A) using in vitro kinase assays and cell-based approaches, we demonstrate here that TBK1 activates mTOR complex 2 (mTORC2) directly to increase Akt phosphorylation. We find that TBK1 and mTOR S2159 phosphorylation promote mTOR-dependent phosphorylation of Akt in response to several growth factors and poly(I:C). Mechanistically, TBK1 co-immunoprecipitates with mTORC2 and phosphorylates mTOR S2159 within mTORC2 in cells. Kinase assays demonstrate that TBK1 and mTOR S2159 phosphorylation increase mTORC2 intrinsic catalytic activity. Growth factors failed to activate TBK1 or increase mTOR S2159 phosphorylation in MEFs. Thus, basal TBK1 activity cooperates with growth factors in parallel to increase mTORC2 (and mTORC1) signaling. Collectively, these results reveal crosstalk between TBK1 and mTOR, key regulatory nodes within two major signaling networks. As TBK1 and mTOR contribute to tumorigenesis and metabolic disorders, these kinases may work together in a direct manner in a variety of physiological and pathological settings.

Keywords:  Akt; TBK1; mTOR; mTORC2; phosphorylation

DOI:  https://doi.org/10.1016/j.jbc.2021.100942
Elife. 2021 Jul 13. pii: e66942. [Epub ahead of print]10

Akt phosphorylates insulin receptor substrate to limit PI3K-mediated PIP3 synthesis.

Alison L Kearney, Dougall M Norris, Milad Ghomlaghi, Martin Kin Lok Wong, Sean J Humphrey, Luke Carroll, Guang Yang, Kristen C Cooke, Pengyi Yang, Thomas A Geddes, Sungyoung Shin, Daniel J Fazakerley, Lan K Nguyen, David E James, James G Burchfield.

  The phosphoinositide 3-kinase (PI3K)-Akt network is tightly controlled by feedback mechanisms that regulate signal flow and ensure signal fidelity. A rapid overshoot in insulin-stimulated recruitment of Akt to the plasma membrane has previously been reported, which is indicative of negative feedback operating on acute timescales. Here, we show that Akt itself engages this negative feedback by phosphorylating insulin receptor substrate (IRS) 1 and 2 on a number of residues. Phosphorylation results in the depletion of plasma membrane-localised IRS1/2, reducing the pool available for interaction with the insulin receptor. Together these events limit plasma membrane-associated PI3K and phosphatidylinositol (3,4,5)-trisphosphate (PIP3) synthesis. We identified two Akt-dependent phosphorylation sites in IRS2 at S306 (S303 in mouse) and S577 (S573 in mouse) that are key drivers of this negative feedback. These findings establish a novel mechanism by which the kinase Akt acutely controls PIP3 abundance, through post-translational modification of the IRS scaffold.

Keywords:  Akt; PI3K; cell biology; computational biology; human; insulin; mouse; phosphorylation; plasma membrane; signal transduction; systems biology

DOI:  https://doi.org/10.7554/eLife.66942
J Endocr Soc. 2021 Aug 01. 5(8): bvab102

Thyroid Hormone Receptor Beta Inhibits PI3K-Akt-mTOR Signaling Axis in Anaplastic Thyroid Cancer via Genomic Mechanisms.

Cole D Davidson, Eric L Bolf, Noelle E Gillis, Lauren M Cozzens, Jennifer A Tomczak, Frances E Carr.

  Thyroid cancer is the most common endocrine malignancy, and the global incidence has increased rapidly over the past few decades. Anaplastic thyroid cancer (ATC) is highly aggressive, dedifferentiated, and patients have a median survival of fewer than 6 months. Oncogenic alterations in ATC include aberrant phosphoinositide 3 kinase (PI3K) signaling through receptor tyrosine kinase (RTK) amplification, loss of phosphoinositide phosphatase expression and function, and protein kinase B (Akt) amplification. Furthermore, the loss of expression of the tumor suppressor thyroid hormone receptor beta (TRβ) is strongly associated with ATC. TRβ is known to suppress PI3K in follicular thyroid cancer and breast cancer by binding to the PI3K regulatory subunit p85α. However, the role of TRβ in suppressing PI3K signaling in ATC is not completely delineated. Here we report that TRβ indeed suppresses PI3K signaling in ATC cell lines through unreported genomic mechanisms, including a decrease in RTK expression and an increase in phosphoinositide and Akt phosphatase expression. Furthermore, the reintroduction and activation of TRβ in ATC cell lines enables an increase in the efficacy of the competitive PI3K inhibitors LY294002 and buparlisib on cell viability, migration, and suppression of PI3K signaling. These findings not only uncover additional tumor suppressor mechanisms of TRβ but shed light on the implication of TRβ status and activation on inhibitor efficacy in ATC tumors.

Keywords:  PI3K; PI3K inhibitor; PI3K phosphatase; anaplastic thyroid cancer; receptor tyrosine kinase; thyroid hormone receptor

DOI:  https://doi.org/10.1210/jendso/bvab102
Nat Commun. 2021 07 12. 12(1): 4245

TSC2 regulates lysosome biogenesis via a non-canonical RAGC and TFEB-dependent mechanism.

Nicola Alesi, Elie W Akl, Damir Khabibullin, Heng-Jia Liu, Anna S Nidhiry, Emma R Garner, Harilaos Filippakis, Hilaire C Lam, Wei Shi, Srinivas R Viswanathan, Manrico Morroni, Shawn M Ferguson, Elizabeth P Henske.

Tuberous Sclerosis Complex (TSC) is caused by TSC1 or TSC2 mutations, resulting in hyperactivation of the mechanistic target of rapamycin complex 1 (mTORC1). Transcription factor EB (TFEB), a master regulator of lysosome biogenesis, is negatively regulated by mTORC1 through a RAG GTPase-dependent phosphorylation. Here we show that lysosomal biogenesis is increased in TSC-associated renal tumors, pulmonary lymphangioleiomyomatosis, kidneys from Tsc2+/- mice, and TSC1/2-deficient cells via a TFEB-dependent mechanism. Interestingly, in TSC1/2-deficient cells, TFEB is hypo-phosphorylated at mTORC1-dependent sites, indicating that mTORC1 is unable to phosphorylate TFEB in the absence of the TSC1/2 complex. Importantly, overexpression of folliculin (FLCN), a GTPase activating protein for RAGC, increases TFEB phosphorylation at the mTORC1 sites in TSC2-deficient cells. Overexpression of constitutively active RAGC is sufficient to relocalize TFEB to the cytoplasm. These findings establish the TSC proteins as critical regulators of lysosomal biogenesis via TFEB and RAGC and identify TFEB as a driver of the proliferation of TSC2-deficient cells.

DOI: https://doi.org/10.1038/s41467-021-24499-6
Mol Cell. 2021 Jul 05. pii: S1097-2765(21)00497-4. [Epub ahead of print]

An mTORC1-GRASP55 signaling axis controls unconventional secretion to reshape the extracellular proteome upon stress.

Julian Nüchel, Marina Tauber, Janica L Nolte, Matthias Mörgelin, Clara Türk, Beate Eckes, Constantinos Demetriades, Markus Plomann.

  Cells communicate with their environment via surface proteins and secreted factors. Unconventional protein secretion (UPS) is an evolutionarily conserved process, via which distinct cargo proteins are secreted upon stress. Most UPS types depend upon the Golgi-associated GRASP55 protein. However, its regulation and biological role remain poorly understood. Here, we show that the mechanistic target of rapamycin complex 1 (mTORC1) directly phosphorylates GRASP55 to maintain its Golgi localization, thus revealing a physiological role for mTORC1 at this organelle. Stimuli that inhibit mTORC1 cause GRASP55 dephosphorylation and relocalization to UPS compartments. Through multiple, unbiased, proteomic analyses, we identify numerous cargoes that follow this unconventional secretory route to reshape the cellular secretome and surfactome. Using MMP2 secretion as a proxy for UPS, we provide important insights on its regulation and physiological role. Collectively, our findings reveal the mTORC1-GRASP55 signaling hub as the integration point in stress signaling upstream of UPS and as a key coordinator of the cellular adaptation to stress.

Keywords:  ECM; GORASP2; GRASP55; Golgi; MMP2; Rapamycin; Tuberous Sclerosis Complex (TSC); cellular stress response; mTORC1; unconventional protein secretion (UPS)

DOI:  https://doi.org/10.1016/j.molcel.2021.06.017
Integr Cancer Ther. 2021 Jan-Dec;20:20 15347354211032283

Treating Alpelisib-Induced Hyperglycemia with Very Low Carbohydrate Diets and Sodium-Glucose Co-Transporter 2 Inhibitors: A Case Series.

Tahj Blow, Parker N Hyde, John N Falcone, Aaron Neinstein, Neil Vasan, Ritika Chitkara, Maurice A Hurd, Sagar Sardesai, Maryam B Lustberg, James H Flory, Jeff S Volek, Marcus D Goncalves.

  Alpelisib is a α-selective phosphatidylinositol 3-kinase (PI3K) inhibitor approved for treatment of postmenopausal women, and men, with hormone receptor positive (HR+), human epidermal growth factor receptor 2 negative (HER2-), PIK3CA-mutated, advanced breast cancer (ABC). Hyperglycemia is a common, on-target adverse effect that impairs treatment efficacy and increases the rate of treatment delays, dose reductions, and discontinuation. Currently, there are no clear guidelines on how to manage hyperglycemia due to alpelisib when metformin is not effective. In this case series, we review 3 subjects with ABC that developed hyperglycemia during alpelisib-fulvestrant therapy and were successfully managed with dietary and pharmacologic interventions. These cases provide anecdotal evidence to support the use of sodium-glucose co-transporter-2 inhibitors (SGLT2i) and very low carbohydrate diets to minimize hyperglycemia during alpelisib therapy.

Keywords:  PI3K inhibitor; SGLT2 inhibitor; alpelisib; hyperglycemia; very-low carbohydrate diet

DOI:  https://doi.org/10.1177/15347354211032283
Front Oncol. 2021 ;11 668247

PI3K Promotes Basal Cell Carcinoma Growth Through Kinase-Induced p21 Degradation.

Rachel Y Chow, Ung Seop Jeon, Taylor M Levee, Gurleen Kaur, Daniel P Cedeno, Linda T Doan, Scott X Atwood.

  Basal cell carcinoma (BCC) is a locally invasive epithelial cancer that is primarily driven by the Hedgehog (HH) pathway. Advanced BCCs are a critical subset of BCCs that frequently acquire resistance to Smoothened (SMO) inhibitors and identifying pathways that bypass SMO could provide alternative treatments for patients with advanced or metastatic BCC. Here, we use a combination of RNA-sequencing analysis of advanced human BCC tumor-normal pairs and immunostaining of human and mouse BCC samples to identify a PI3K pathway expression signature in BCC. Pharmacological inhibition of PI3K activity in BCC cells significantly reduces cell proliferation and HH signaling. However, treatment of Ptch1fl/fl ; Gli1-CreERT2 mouse BCCs with the PI3K inhibitor BKM120 results in a reduction of tumor cell growth with no significant effect on HH signaling. Downstream PI3K components aPKC and Akt1 showed a reduction in active protein, whereas their substrate, cyclin-dependent kinase inhibitor p21, showed a concomitant increase in protein stability. Our results suggest that PI3K promotes BCC tumor growth by kinase-induced p21 degradation without altering HH signaling.

Keywords:  PI3K - AKT pathway; atypical PKCι; basal cell carcinoma; hedgehog; p21

DOI:  https://doi.org/10.3389/fonc.2021.668247
Exp Cell Res. 2021 Jul 13. pii: S0014-4827(21)00263-9. [Epub ahead of print] 112731

Modulation of Akt vs Stat3 activity by the focal adhesion kinase in non-neoplastic mouse fibroblasts.

Mulu Geletu, Hanad Adan, Maximillian Niit, Rozanne Arulanandam, Esther Carefoot, Victoria Hoskin, Diana Sina, Bruce Elliott, Patrick Gunning, Leda Raptis.

Adhesion of cells to each other and to the extracellular matrix (ECM) are both required for cellular functions. Cell-to-cell adhesion is mediated by cadherins, and their engagement triggers the activation of Stat3, which offers a potent survival signal. Adhesion to the ECM on the other hand, activates FAK which attracts and activates Src, as well as receptor tyrosine kinases (RTKs), the PI3k/Akt and Ras/Erk pathways. However, the effect of cell density upon FAK and Akt activity has not been examined. We now demonstrate that, interestingly, despite being potent Stat3 activators, Src and RTKs are unable to activate Stat3 in sparsely growing (i.e., without cadherin engagement), non-neoplastic cells attached to the ECM. In contrast, cell aggregation (i.e., cadherin engagement in the absence of adhesion to a solid substratum) was found to activate both Stat3 and Akt. Pharmacologic or genetic reduction of FAK activity abolished Akt activity at low densities, indicating that FAK is an important activator of Akt in this setting. Notably, FAK knockout increased cellular sensitivity to the Stat3 inhibitor CPA7, while FAK reintroduction restored resistance to this drug. These findings suggest a complementary role of integrin/FAK/Akt and cadherin/Stat3-mediated pro-survival pathways, which may be of significance during neoplastic transformation and metastasis.

DOI: https://doi.org/10.1016/j.yexcr.2021.112731
Front Pediatr. 2021 ;9 688022

Two Monogenetic Disorders, Activated PI3-Kinase-δ Syndrome 2 and Smith-Magenis Syndrome, in One Patient: Case Report and a Literature Review of Neurodevelopmental Impact in Primary Immunodeficiencies Associated With Disturbed PI3K Signaling.

Nidia Moreno-Corona, Loïc Chentout, Lucie Poggi, Romane Thouenon, Cecile Masson, Melanie Parisot, Lou Le Mouel, Capucine Picard, Isabelle André, Marina Cavazzana, Laurence Perrin, Anne Durandy, Saba Azarnoush, Sven Kracker.

  Activated PI3-kinase-δ syndrome 2 (APDS2) is caused by autosomal dominant mutations in the PIK3R1 gene encoding the p85α, p55α, and p50α regulatory subunits. Most diagnosed APDS2 patients carry mutations affecting either the splice donor or splice acceptor sites of exon 11 of the PIK3R1 gene responsible for an alternative splice product and a shortened protein. The clinical presentation of APDS2 patients is highly variable, ranging from mild to profound combined immunodeficiency features as massive lymphoproliferation, increased susceptibility to bacterial and viral infections, bronchiectasis, autoimmune manifestations, and occurrence of cancer. Non-immunological features such as growth retardation and neurodevelopmental delay have been reported for APDS2 patients. Here, we describe a patient suffering from an APDS2 associated with a Smith-Magenis syndrome (SMS), a complex genetic disorder affecting, among others, neurological manifestations and review the literature describing neurodevelopmental impacts in APDS2 and other PIDs/monogenetic disorders associated with dysregulated PI3K signaling.

Keywords:  APDS2; PI3K signaling; PIK3R1; neurodevelopmental impact; primary immunodeficiency

DOI:  https://doi.org/10.3389/fped.2021.688022
JCO Precis Oncol. 2021 ;pii: PO.20.00424. [Epub ahead of print]5

Plasma Cell-Free DNA Profiling of PTEN-PI3K-AKT Pathway Aberrations in Metastatic Castration-Resistant Prostate Cancer.

Edmond M Kwan, Chao Dai, Heidi Fettke, Christine Hauser, Maria M Docanto, Patricia Bukczynska, Nicole Ng, Siavash Foroughi, Lisa-Jane K Graham, Kate Mahon, Winston Tan, Xiaohong Wang, Zhixin Zhao, Tiantian Zheng, Kemin Zhou, Jianjun Yu, Pan Du, Lisa G Horvath, Shidong Jia, Manish Kohli, Arun A Azad.

Tumor tissue from metastatic castration-resistant prostate cancer (mCRPC) harbors frequent copy number variations (CNVs) in the PTEN-PI3K-AKT pathway. However, identifying CNVs in plasma cell-free DNA (cfDNA) has proven to be challenging. With emerging data supporting Akt inhibition in PTEN-deficient mCRPC, we profiled PTEN-PI3K-AKT pathway aberrations in patients with mCRPC using a novel cfDNA assay optimized for CNV detection.METHODS: A next-generation sequencing-based cfDNA assay was used to profile 231 patients with mCRPC from two independent cohorts (Australian, n = 78; United States, n = 153). PTEN-PI3K-AKT pathway genomic aberrations were correlated with clinical outcomes, including progression-free survival and overall survival (OS).
RESULTS: PTEN loss and PIK3CA gain were detected in 37% (85 of 231) and 17% (39 of 231) of patients, respectively. Poorer outcomes were observed in patients with PTEN-PI3K-AKT pathway aberrations, including those with dual PTEN loss and PIK3CA gain (hazard ratio 2.3, 95% CI 1.2 to 4.4). Cumulative CNV burden in the PTEN-PI3K-AKT and androgen receptor (AR) pathways was associated with significantly worse clinical outcomes (0 v 1 v ≥ 2 CNVs in Australian cohort: median OS 33.5 v 17.2 v 9.7 months, P < .001; 0 v 1 v ≥ 2 CNVs in US cohort: median OS 35.5 v 14.3 v 9.2 months, P < .001). Notably, 21% (31 of 146) of PTEN-neutral patients harbored alternative PTEN-PI3K-AKT pathway aberrations.
CONCLUSION: PTEN-PI3K-AKT pathway CNVs were readily detected using our cfDNA assay, with the prevalence of PTEN loss comparable with tissue-based studies. Additional PTEN-PI3K-AKT pathway aberrations were found in one fifth of PTEN-neutral cases. Concurrent CNVs in the PTEN-PI3K-AKT and AR pathways portended poor survival, and identifying this high-risk patient subset for dual AR/Akt inhibition may optimize precision treatment with Akt inhibitors in mCRPC.

DOI: https://doi.org/10.1200/PO.20.00424
Front Pediatr. 2021 ;9 652405

Activated PI3Kinase Delta Syndrome-A Multifaceted Disease.

Romane Thouenon, Nidia Moreno-Corona, Lucie Poggi, Anne Durandy, Sven Kracker.

  Autosomal dominant gain-of-function mutations in the PIK3CD gene encoding the catalytic subunit p110δ of phosphoinositide 3-kinase-δ (PI3K-δ) or autosomal dominant loss-of-function mutations in the PIK3R1 gene encoding the p85α, p55α and p50α regulatory subunits cause Activated PI3-kinase-δ syndrome (APDS; referred as type 1 APDS and type 2 APDS, respectively). Consequences of these mutations are PI3K-δ hyperactivity. Clinical presentation described for both types of APDS patients is very variable, ranging from mild or asymptomatic features to profound combined immunodeficiency. Massive lymphoproliferation, bronchiectasis, increased susceptibility to bacterial and viral infections and, at a lesser extent, auto-immune manifestations and occurrence of cancer, especially B cell lymphoma, have been described for both types of APDS patients. Here, we review clinical presentation and treatment options as well as fundamental immunological and biological features associated to PI3K-δ increased signaling.

Keywords:  PI3K signaling; PIK3CD; PIK3R1; lymphoproliferation; primary immunodeficiency

DOI:  https://doi.org/10.3389/fped.2021.652405
Nat Commun. 2021 07 12. 12(1): 4262

Morphological screening of mesenchymal mammary tumor organoids to identify drugs that reverse epithelial-mesenchymal transition.

Na Zhao, Reid T Powell, Xueying Yuan, Goeun Bae, Kevin P Roarty, Fabio Stossi, Martina Strempfl, Michael J Toneff, Hannah L Johnson, Sendurai A Mani, Philip Jones, Clifford C Stephan, Jeffrey M Rosen.

The epithelial-mesenchymal transition (EMT) has been implicated in conferring stem cell properties and therapeutic resistance to cancer cells. Therefore, identification of drugs that can reprogram EMT may provide new therapeutic strategies. Here, we report that cells derived from claudin-low mammary tumors, a mesenchymal subtype of triple-negative breast cancer, exhibit a distinctive organoid structure with extended "spikes" in 3D matrices. Upon a miR-200 induced mesenchymal-epithelial transition (MET), the organoids switch to a smoother round morphology. Based on these observations, we developed a morphological screening method with accompanying analytical pipelines that leverage deep neural networks and nearest neighborhood classification to screen for EMT-reversing drugs. Through screening of a targeted epigenetic drug library, we identified multiple class I HDAC inhibitors and Bromodomain inhibitors that reverse EMT. These data support the use of morphological screening of mesenchymal mammary tumor organoids as a platform to identify drugs that reverse EMT.

DOI: https://doi.org/10.1038/s41467-021-24545-3
J Clin Immunol. 2021 Jul 16.

BCG Vaccine-Associated Complications in Patients with PTEN Hamartoma Tumor Syndrome.

Henry Taylor, Dominik Aschenbrenner, Mike Thomson, Hannah Chen, Holm H Uhlig.

DOI: https://doi.org/10.1007/s10875-021-01100-9
Dev Cell. 2021 Jul 12. pii: S1534-5807(21)00523-2. [Epub ahead of print]56(13): 1875-1883

Microenvironmental control of cell fate decisions in mammary gland development and cancer.

Gat Rauner, Charlotte Kuperwasser.

  Cell fate decisions are critical for adequate tissue development, maintenance and regeneration. In the mammary gland, epithelial cell fates are tightly controlled by the microenvironment. Here, we review how cell fate decisions are regulated by components of the microenvironment during mammary gland development and how pathological changes in the microenvironment can alter cell fates, leading to malignancy. Specifically, we describe the current understanding of how mammary cell fate is controlled and directed by three elements: the extracellular matrix, the immune microenvironment, and hormones-and how these elements can converge to create microenvironments that promote a fourth element: DNA damage.

Keywords:  Breast; Breast cancer; DNA damage; Development; ECM; Mammary gland; Microenvironment; Obesity

DOI:  https://doi.org/10.1016/j.devcel.2021.06.016
Cancer Res. 2021 Jul 13. pii: canres.1208.2021. [Epub ahead of print]

Cell line-specific network models of ER+ breast cancer identify potential PI3Kα inhibitor resistance mechanisms and drug combinations.

Jorge Gómez Tejeda Zañudo, Pingping Mao, Clara Alcon, Kailey Kowalski, Gabriela N Johnson, Guotai Xu, Jose Baselga, Maurizio Scaltriti, Anthony Letai, Joan Montero, Réka Albert, Nikhil Wagle.

Durable control of invasive solid tumors necessitates identifying therapeutic resistance mechanisms and effective drug combinations. In this work, we used a network-based mathematical model to identify sensitivity regulators and drug combinations for the PI3Kα inhibitor alpelisib in ER+ PIK3CA mutant breast cancer. The model-predicted efficacious combination of alpelisib and BH3 mimetics, e.g., MCL1 inhibitors, was experimentally validated in ER+ breast cancer cell lines. Consistent with the model, FOXO3 downregulation reduced sensitivity to alpelisib, revealing a novel potential resistance mechanism. Cell line-specific sensitivity to combinations of alpelisib and BH3 mimetics depended on which BCL-2 family members were highly expressed. Based on these results, newly developed cell line-specific network models were able to recapitulate the observed differential response to alpelisib and BH3 mimetics. This approach illustrates how network-based mathematical models can contribute to overcoming the challenge of cancer drug resistance.

DOI: https://doi.org/10.1158/0008-5472.CAN-21-1208
JCO Precis Oncol. 2021 ;pii: PO.20.00184. [Epub ahead of print]5

Utility of Serial cfDNA NGS for Prospective Genomic Analysis of Patients on a Phase I Basket Study.

Lillian M Smyth, Jonathan B Reichel, Jiabin Tang, Juber Ahamad A Patel, Fanli Meng, Duygu S Selcuklu, Brian Houck-Loomis, Daoqi You, Aliaksandra Samoila, Gaia Schiavon, Bob T Li, Pedram Razavi, Salvatore Piscuoglio, Jorge S Reis-Filho, Barry S Taylor, José Baselga, David B Solit, David M Hyman, Michael F Berger, Sarat Chandarlapaty.

PURPOSE: Cell-free DNA (cfDNA) analysis offers a noninvasive means to access the tumor genome. Despite limited sensitivity of broad-panel sequencing for detecting low-frequency mutations in cfDNA, it may enable more comprehensive genomic characterization in patients with sufficiently high disease burden. We investigated the utility of large-panel cfDNA sequencing in patients enrolled to a Phase I AKT1-mutant solid tumor basket study.METHODS: Patients had AKT1 E17K-mutant solid tumors and were treated on the multicenter basket study (ClinicalTrials.gov identifier: NCT01226316) of capivasertib, an AKT inhibitor. Serial plasma samples were prospectively collected and sequenced using exon-capture next-generation sequencing (NGS) analysis of 410 genes (Memorial Sloan Kettering [MSK]-Integrated Molecular Profiling of Actionable Cancer Target [IMPACT]) and allele-specific droplet digital polymerase chain reaction (ddPCR) for AKT1 E17K. Tumor DNA (tDNA) NGS (MSK-IMPACT) was also performed on available pretreatment tissue biopsy specimens.
RESULTS: Among 25 patients, pretreatment plasma samples were sequenced to an average coverage of 504×. Somatic mutations were called in 20/25 (80%), with mutant allele fractions highly concordant with ddPCR of AKT1 E17K (r 2 = 0.976). Among 17 of 20 cfDNA-positive patients with available tDNA for comparison, mutational concordance was acceptable, with 82% of recurrent mutations shared between tissue and plasma. cfDNA NGS captured additional tumor heterogeneity, identifying mutations not observed in tDNA in 38% of patients, and revealed oncogenic mutations in patients without available baseline tDNA. Longitudinal cfDNA NGS (n = 98 samples) revealed distinct patterns of clonal dynamics in response to therapy.
CONCLUSION: Large gene panel cfDNA NGS is feasible for patients with high disease burden and is concordant with single-analyte approaches, providing a robust alternative to ddPCR with greater breadth. cfDNA NGS can identify heterogeneity and potentially biologically informative and clinically relevant alterations.

DOI: https://doi.org/10.1200/PO.20.00184
Bioinformatics. 2021 Jul 09. pii: btab503. [Epub ahead of print]

UCSC Cell Browser: Visualize Your Single-Cell Data.

Matthew L Speir, Aparna Bhaduri, Nikolay S Markov, Pablo Moreno, Tomasz J Nowakowski, Irene Papatheodorou, Alex A Pollen, Brian J Raney, Lucas Seninge, W James Kent, Maximilian Haeussler.

SUMMARY: As the use of single-cell technologies has grown, so has the need for tools to explore these large, complicated datasets. The UCSC Cell Browser is a tool that allows scientists to visualize gene expression and metadata annotation distribution throughout a single-cell dataset or multiple datasets.AVAILABILITY AND IMPLEMENTATION: We provide the UCSC Cell Browser as a free website where scientists can explore a growing collection of single-cell datasets and a freely available python package for scientists to create stable, self-contained visualizations for their own single-cell datasets. Learn more at https://cells.ucsc.edu.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btab503
Nat Commun. 2021 07 09. 12(1): 4227

mTORC1 activity regulates post-translational modifications of glycine decarboxylase to modulate glycine metabolism and tumorigenesis.

Rui Liu, Lin-Wen Zeng, Rong Gong, Fanen Yuan, Hong-Bing Shu, Shu Li.

Glycine decarboxylase (GLDC) is a key enzyme of glycine cleavage system that converts glycine into one-carbon units. GLDC is commonly up-regulated and plays important roles in many human cancers. Whether and how GLDC is regulated by post-translational modifications is unknown. Here we report that mechanistic target of rapamycin complex 1 (mTORC1) signal inhibits GLDC acetylation at lysine (K) 514 by inducing transcription of the deacetylase sirtuin 3 (SIRT3). Upon inhibition of mTORC1, the acetyltransferase acetyl-CoA acetyltransferase 1 (ACAT1) catalyzes GLDC K514 acetylation. This acetylation of GLDC impairs its enzymatic activity. In addition, this acetylation of GLDC primes for its K33-linked polyubiquitination at K544 by the ubiquitin ligase NF-X1, leading to its degradation by the proteasomal pathway. Finally, we find that GLDC K514 acetylation inhibits glycine catabolism, pyrimidines synthesis and glioma tumorigenesis. Our finding reveals critical roles of post-translational modifications of GLDC in regulation of its enzymatic activity, glycine metabolism and tumorigenesis, and provides potential targets for therapeutics of cancers such as glioma.

DOI: https://doi.org/10.1038/s41467-021-24321-3
Gynecol Oncol. 2021 Jul 10. pii: S0090-8258(21)00538-2. [Epub ahead of print]

The effectiveness of monotherapy with PI3K/AKT/mTOR pathway inhibitors in ovarian cancer: A meta-analysis.

Phyllis van der Ploeg, Aniek Uittenboogaard, Anna M J Thijs, Hans M Westgeest, Ingrid A Boere, Sandrina Lambrechts, Anja van de Stolpe, Ruud L M Bekkers, Jurgen M J Piek.

  OBJECTIVE: To determine the clinical benefit of monotherapy with PI3K/AKT/mTOR inhibitors in patients diagnosed with advanced or recurrent ovarian cancer and to investigate the predictive value of current PI3K/AKT/mTOR biomarkers on therapy response.METHODS: A systematic search was conducted in PubMed, Embase and the Cochrane Library for articles reporting on treatment with PI3K/AKT/mTOR inhibitors in ovarian cancer. The primary endpoint was defined as the clinical benefit rate (CBR), including the proportion of patients with complete (CR) and partial response (PR) and stable disease (SD). Secondary endpoints included the overall response rate (ORR, including CR and PR) and drug-related grade 3 and 4 adverse events.
RESULTS: We included 233 patients from 19 studies and observed a pooled CBR of 32% (95% CI 20-44%) and ORR of 3% (95% CI 0-6%) in advanced or recurrent ovarian cancer patients treated with PI3K/AKT/mTOR inhibitors. Subgroup analysis tended to favor the studies who selected patients based on current PI3K/AKT/mTOR biomarker criteria (e.g. genomic alterations or loss of PTEN protein expression), but the difference in CBR was not statistically significant from studies with unselected populations (respectively, CBR of 42% (95% CI 23-62%) and 27% (95% CI 14-42%), P = 0.217). To better reflect true patient benefit, we excluded SD <6 months as a beneficial outcome which resulted in a pooled CBR of 7% (95% CI 2-13%). The overall proportion of patients with drug-related grade 3 and 4 adverse events was 36%.
CONCLUSIONS: The efficacy of monotherapy with PI3K/AKT/mTOR inhibitors in advanced recurrent ovarian cancer patients is limited to a small subgroup and selection of patients with the use of current biomarkers did not improved the CBR significantly. Given the toxicity profile, we suggest that current treatment with PI3K/AKT/mTOR inhibitors should not be initiated unless in clinical trials. Furthermore, improved biomarkers to measure functional PI3K/AKT/mTOR pathway activity are needed to optimize patient selection.

Keywords:  Akt; Mammalian target of rapamycin; Ovarian cancer; Phosphatidylinositol-3-kinase; Signal transduction pathway; Targeted therapy

DOI:  https://doi.org/10.1016/j.ygyno.2021.07.008
Hum Mol Genet. 2021 Jul 12. pii: ddab196. [Epub ahead of print]

Functional assessment of two variants of unknown significance in TEK by endothelium-specific expression in zebrafish embryos.

Lorenz M Bell, Annegret Holm, Uta Matysiak, Wolfgang Driever, Jochen Rößler, Denny Schanze, Ilse Wieland, Charlotte M Niemeyer, Martin Zenker, Friedrich G Kapp.

Vascular malformations are most often caused by somatic mutations of the PI3K/mTOR and the RAS signaling pathways, which can be identified in the affected tissue. Venous malformations commonly harbor PIK3CA and TEK mutations, whereas arteriovenous malformations are usually caused by BRAF, RAS, or MAP2K1 mutations. Correct identification of the underlying mutation is of increasing importance, since targeted treatments are becoming more and more relevant, especially in patients with extensive vascular malformations. However, variants of unknown significance are often identified and their pathogenicity and response to targeted therapy cannot be precisely predicted. Here we show, that zebrafish embryos can be used to rapidly assess the pathogenicity of novel variants of unknown significance in TEK, encoding for the receptor TIE2, present on endothelial cells of venous malformations. Endothelium-specific overexpression of TEK mutations leads to robust induction of venous malformations whereas MAP2K1 mutations cause arteriovenous malformations in our zebrafish model. TEK mutations are often found as double mutations in cis; using our model, we show that double mutations have an additive effect in inducing venous malformations compared to the respective single variants. The clinically established mTOR-inhibitor sirolimus (rapamycin) efficiently abrogates the development of venous malformations in this zebrafish model. In summary, endothelium-specific overexpression of patient-derived TEK variants in the zebrafish model allows assessment of their pathogenic significance as well as testing of candidate drugs in a personalized and mutation-specific approach.

DOI: https://doi.org/10.1093/hmg/ddab196
Nat Commun. 2021 07 15. 12(1): 4339

Redefining the specificity of phosphoinositide-binding by human PH domain-containing proteins.

Nilmani Singh, Adriana Reyes-Ordoñez, Michael A Compagnone, Jesus F Moreno, Benjamin J Leslie, Taekjip Ha, Jie Chen.

Pleckstrin homology (PH) domains are presumed to bind phosphoinositides (PIPs), but specific interaction with and regulation by PIPs for most PH domain-containing proteins are unclear. Here we employ a single-molecule pulldown assay to study interactions of lipid vesicles with full-length proteins in mammalian whole cell lysates. Of 67 human PH domain-containing proteins initially examined, 36 (54%) are found to have affinity for PIPs with various specificity, the majority of which have not been reported before. Further investigation of ARHGEF3 reveals distinct structural requirements for its binding to PI(4,5)P2 and PI(3,5)P2, and functional relevance of its PI(4,5)P2 binding. We generate a recursive-learning algorithm based on the assay results to analyze the sequences of 242 human PH domains, predicting that 49% of them bind PIPs. Twenty predicted binders and 11 predicted non-binders are assayed, yielding results highly consistent with the prediction. Taken together, our findings reveal unexpected lipid-binding specificity of PH domain-containing proteins.

DOI: https://doi.org/10.1038/s41467-021-24639-y
Diabetes. 2021 Jul 15. pii: db210160. [Epub ahead of print]

Subcutaneous adipose tissue metabolic function and insulin sensitivity in people with obesity.

Han-Chow E Koh, Stephan van Vliet, Terri A Pietka, Gretchen A Meyer, Babak Razani, Richard Laforest, Robert J Gropler, Bettina Mittendorfer.

We used stable isotope-labeled glucose and palmitate tracer infusions, a hyperinsulinemic-euglycemic clamp, positron-emission tomography of muscles and adipose tissue after [18F]fluorodeoxyglucose and [15O]water injections, and subcutaneous adipose tissue (SAT) biopsy to test the hypotheses that: i) increased glucose uptake in SAT is responsible for high insulin-stimulated whole-body glucose uptake in people with obesity who are insulin-sensitive, and ii) putative SAT factors thought to cause insulin resistance are present in people with obesity who are insulin-resistant but not in those who are insulin-sensitive. We found high insulin-stimulated whole-body glucose uptake in insulin-sensitive participants with obesity was not due to channeling of glucose into SAT, but was due to high insulin-stimulated muscle glucose uptake. Furthermore, insulin-stimulated muscle glucose uptake was not different between insulin-sensitive obese and lean participants even though adipocytes were larger, SAT perfusion and oxygenation were lower, and markers of SAT inflammation, fatty acid appearance in plasma in relation to fat-free mass, and plasma fatty acid concentration were higher in the insulin-sensitive obese than lean participants. In addition, we observed only marginal or no differences in adipocyte size, SAT perfusion and oxygenation, and markers of SAT inflammation between insulin-resistant and insulin-sensitive obese participants. Plasma fatty acid concentration was also not different between insulin-sensitive and insulin-resistant obese participants even though SAT was resistant to the inhibitory effect of insulin on lipolysis in the insulin-resistant obese group. These data suggest several putative SAT factors that are commonly implicated in causing insulin resistance are normal consequences of SAT expansion unrelated to insulin resistance.

DOI: https://doi.org/10.2337/db21-0160
Breast Cancer Res Treat. 2021 Jul 15.

Final results of the double-blind placebo-controlled randomized phase 2 LOTUS trial of first-line ipatasertib plus paclitaxel for inoperable locally advanced/metastatic triple-negative breast cancer.

Rebecca Dent, Mafalda Oliveira, Steven J Isakoff, Seock-Ah Im, Marc Espié, Sibel Blau, Antoinette R Tan, Cristina Saura, Matthew J Wongchenko, Na Xu, Denise Bradley, Sarah-Jayne Reilly, Aruna Mani, Sung-Bae Kim, .

  PURPOSE: In LOTUS (NCT02162719), adding the oral AKT inhibitor ipatasertib to first-line paclitaxel for locally advanced/metastatic triple-negative breast cancer (aTNBC) improved progression-free survival (PFS; primary endpoint), with an enhanced effect in patients with PIK3CA/AKT1/PTEN-altered tumors (FoundationOne next-generation sequencing [NGS] assay). We report final overall survival (OS) results.METHODS: Eligible patients had measurable previously untreated aTNBC. Patients were stratified by prior (neo)adjuvant therapy, chemotherapy-free interval, and tumor immunohistochemistry PTEN status, and were randomized 1:1 to paclitaxel 80 mg/m2 (days 1, 8, 15) plus ipatasertib 400 mg or placebo (days 1-21) every 28 days until disease progression or unacceptable toxicity. OS (intent-to-treat [ITT], immunohistochemistry PTEN-low, and PI3K/AKT pathway-activated [NGS PIK3CA/AKT1/PTEN-altered] populations) was a secondary endpoint.
RESULTS: Median follow-up was 19.0 versus 16.0 months in the ipatasertib-paclitaxel versus placebo-paclitaxel arms, respectively. In the ITT population (n = 124), median OS was numerically longer with ipatasertib-paclitaxel than placebo-paclitaxel (hazard ratio 0.80, 95% CI 0.50-1.28; median 25.8 vs 16.9 months, respectively; 1-year OS 83% vs 68%). Likewise, median OS favored ipatasertib-paclitaxel in the PTEN-low (n = 48; 23.1 vs 15.8 months; hazard ratio 0.83) and PIK3CA/AKT1/PTEN-altered (n = 42; 25.8 vs 22.1 months; hazard ratio 1.13) subgroups. The ipatasertib-paclitaxel safety profile was unchanged.
CONCLUSIONS: Final OS results show a numerical trend favoring ipatasertib-paclitaxel and median OS exceeding 2 years with ipatasertib-paclitaxel. Overall, results are consistent with the reported PFS benefit; interpretation within biomarker-defined subgroups is complicated by small sample sizes and TNBC heterogeneity.

Keywords:  First-line therapy; Ipatasertib; Oral; PI3K/AKT; Triple-negative breast cancer

DOI:  https://doi.org/10.1007/s10549-021-06143-5
Diabetes. 2021 Jul 08. pii: db201212. [Epub ahead of print]

Insulin Resistance in Skeletal Muscle Selectively Protects the Heart in Response to Metabolic Stress.

Dandan Jia, Jun Zhang, Xueling Liu, John-Paul Andersen, Zhenjun Tian, Jia Nie, Yuguang Shi.

Obesity and type 2 diabetes mellitus (T2DM) are the leading causes of cardiovascular morbidity and mortality. Although insulin resistance is believed to underlie these disorders, anecdotal evidence contradicts this common belief. Accordingly, obese patients with cardiovascular disease have better prognoses relative to leaner patients with the same diagnoses, whereas treatment of T2DM patients with thiazolidines, one of the popular insulin sensitizer drugs, significantly increases the risk of heart failure. Using mice with skeletal muscle-specific ablation of the insulin receptor gene (MIRKO), we addressed this paradox by demonstrating that insulin signaling in skeletal muscles specifically mediated crosstalk with the heart, but not other metabolic tissues, to prevent cardiac dysfunction in response to metabolic stress. Despite severe hyperinsulinemia and aggregating obesity, MIRKO mice were protected from myocardial insulin resistance, mitochondrial dysfunction, and metabolic reprogramming in response to diet-induced obesity (DIO). Consequently, the MIRKO mice were also protected from myocardial inflammation, cardiomyopathy, and left ventricle dysfunction. Together, our findings suggest that insulin resistance in skeletal muscle functions as a double-edged sword in metabolic diseases.Obesity and type 2 diabetes mellitus (T2DM) are the leading causes of cardiovascular morbidity and mortality. Although insulin resistance is believed to underlie these disorders, anecdotal evidence contradicts this common belief. Accordingly, obese patients with cardiovascular disease have better prognoses relative to leaner patients with the same diagnoses, whereas treatment of T2DM patients with thiazolidines, one of the popular insulin sensitizer drugs, significantly increases the risk of heart failure. Using mice with skeletal muscle-specific ablation of the insulin receptor gene (MIRKO), we addressed this paradox by demonstrating that insulin signaling in skeletal muscles specifically mediated crosstalk with the heart, but not other metabolic tissues, to prevent cardiac dysfunction in response to metabolic stress. Despite severe hyperinsulinemia and aggregating obesity, MIRKO mice were protected from myocardial insulin resistance, mitochondrial dysfunction, and metabolic reprogramming in response to diet-induced obesity (DIO). Consequently, the MIRKO mice were also protected from myocardial inflammation, cardiomyopathy, and left ventricle dysfunction. Together, our findings suggest that insulin resistance in skeletal muscle functions as a double-edged sword in metabolic diseases.

DOI: https://doi.org/10.2337/db20-1212
Lancet. 2021 Jul 10. pii: S0140-6736(21)00580-8. [Epub ahead of print]398(10295): 131-142

Ipatasertib plus abiraterone and prednisolone in metastatic castration-resistant prostate cancer (IPATential150): a multicentre, randomised, double-blind, phase 3 trial.

Christopher Sweeney, Sergio Bracarda, Cora N Sternberg, Kim N Chi, David Olmos, Shahneen Sandhu, Christophe Massard, Nobuaki Matsubara, Boris Alekseev, Francis Parnis, Vagif Atduev, Gary L Buchschacher, Rustem Gafanov, Luis Corrales, Michael Borre, Daniil Stroyakovskiy, Gustavo Vasconcelos Alves, Evangelos Bournakis, Javier Puente, Marie-Laurence Harle-Yge, Jorge Gallo, Geng Chen, Justin Hanover, Matthew J Wongchenko, Josep Garcia, Johann S de Bono.

BACKGROUND: The PI3K/AKT and androgen-receptor pathways are dysregulated in metastatic castration-resistant prostate cancers (mCRPCs); tumours with functional PTEN-loss status have hyperactivated AKT signalling. Dual pathway inhibition with AKT inhibitor ipatasertib plus abiraterone might have greater benefit than abiraterone alone. We aimed to compare ipatasertib plus abiraterone with placebo plus abiraterone in patients with previously untreated mCRPC with or without tumour PTEN loss.METHODS: We did a randomised, double-blind, phase 3 trial at 200 sites across 26 countries or regions. Patients aged 18 years or older with previously untreated asymptomatic or mildly symptomatic mCRPC who had progressive disease and Eastern Collaborative Oncology Group performance status of 0 or 1 were randomly assigned (1:1; permuted block method) to receive ipatasertib (400 mg once daily orally) plus abiraterone (1000 mg once daily orally) and prednisolone (5 mg twice a day orally) or placebo plus abiraterone and prednisolone (with the same dosing schedule). Patients received study treatment until disease progression, intolerable toxicity, withdrawal from the study, or study completion. Stratification factors were previous taxane-based therapy for hormone-sensitive prostate cancer, type of progression, presence of visceral metastasis, and tumour PTEN-loss status by immunohistochemistry. Patients, investigators, and the study sponsor were masked to the treatment allocation. The coprimary endpoints were investigator-assessed radiographical progression-free survival in the PTEN-loss-by-immunohistochemistry population and in the intention-to-treat population. This study is ongoing and is registered with ClinicalTrials.gov, NCT03072238.
FINDINGS: Between June 30, 2017, and Jan 17, 2019, 1611 patients were screened for eligibility and 1101 (68%) were enrolled; 554 (50%) were assigned to the placebo-abiraterone group and 547 (50%) to the ipatasertib-abiraterone group. At data cutoff (March 16, 2020), median follow-up duration was 19 months (range 0-33). In the 521 (47%) patients who had tumours with PTEN loss by immunohistochemistry (261 in the placebo-abiraterone group and 260 in the ipatasertib-abiraterone group), median radiographical progression-free survival was 16·5 months (95% CI 13·9-17·0) in the placebo-abiraterone group and 18·5 months (16·3-22·1) in the ipatasertib-abiraterone group (hazard ratio [HR] 0·77 [95% CI 0·61-0·98]; p=0·034; significant at α=0·04). In the intention-to-treat population, median progression-free survival was 16·6 months (95% CI 15·6-19·1) in the placebo-abiraterone group and 19·2 months (16·5-22·3) in the ipatasertib-abiraterone group (HR 0·84 [95% CI 0·71-0·99]; p=0·043; not significant at α=0·01). Grade 3 or higher adverse events occurred in 213 (39%) of 546 patients in the placebo-abiraterone group and in 386 (70%) of 551 patients in the ipatasertib-abiraterone group; adverse events leading to discontinuation of placebo or ipatasertib occurred in 28 (5%) in the placebo-abiraterone group and 116 (21%) in the ipatasertib-abiraterone group. Deaths due to adverse events deemed related to treatment occurred in two patients (<1%; acute myocardial infarction [n=1] and lower respiratory tract infection [n=1]) in the placebo-abiraterone group and in two patients (<1%; hyperglycaemia [n=1] and chemical pneumonitis [n=1]) in the ipastasertb-abiraterone group.
INTERPRETATION: Ipatasertib plus abiraterone significantly improved radiographical progression-free survival compared with placebo plus abiraterone among patients with mCRPC with PTEN-loss tumours, but there was no significant difference between the groups in the intention-to-treat population. Adverse events were consistent with the known safety profiles of each agent. These data suggest that combined AKT and androgen-receptor signalling pathway inhibition with ipatasertib and abiraterone is a potential treatment for men with PTEN-loss mCRPC, a population with a poor prognosis.
FUNDING: F Hoffmann-La Roche and Genentech.

DOI: https://doi.org/10.1016/S0140-6736(21)00580-8
Nat Rev Mol Cell Biol. 2021 Jul 16.

Translational control of stem cell function.

James A Saba, Kifayathullah Liakath-Ali, Rachel Green, Fiona M Watt.

Stem cells are characterized by their ability to self-renew and differentiate into many different cell types. Research has focused primarily on how these processes are regulated at a transcriptional level. However, recent studies have indicated that stem cell behaviour is strongly coupled to the regulation of protein synthesis by the ribosome. In this Review, we discuss how different translation mechanisms control the function of adult and embryonic stem cells. Stem cells are characterized by low global translation rates despite high levels of ribosome biogenesis. The maintenance of pluripotency, the commitment to a specific cell fate and the switch to cell differentiation depend on the tight regulation of protein synthesis and ribosome biogenesis. Translation regulatory mechanisms that impact on stem cell function include mTOR signalling, ribosome levels, and mRNA and tRNA features and amounts. Understanding these mechanisms important for stem cell self-renewal and differentiation may also guide our understanding of cancer grade and metastasis.

DOI: https://doi.org/10.1038/s41580-021-00386-2
Nat Commun. 2021 07 09. 12(1): 4217

Multiplexed functional genomic analysis of 5' untranslated region mutations across the spectrum of prostate cancer.

Yiting Lim, Sonali Arora, Samantha L Schuster, Lukas Corey, Matthew Fitzgibbon, Cynthia L Wladyka, Xiaoying Wu, Ilsa M Coleman, Jeffrey J Delrow, Eva Corey, Lawrence D True, Peter S Nelson, Gavin Ha, Andrew C Hsieh.

The functional consequences of genetic variants within 5' untranslated regions (UTRs) on a genome-wide scale are poorly understood in disease. Here we develop a high-throughput multi-layer functional genomics method called PLUMAGE (Pooled full-length UTR Multiplex Assay on Gene Expression) to quantify the molecular consequences of somatic 5' UTR mutations in human prostate cancer. We show that 5' UTR mutations can control transcript levels and mRNA translation rates through the creation of DNA binding elements or RNA-based cis-regulatory motifs. We discover that point mutations can simultaneously impact transcript and translation levels of the same gene. We provide evidence that functional 5' UTR mutations in the MAP kinase signaling pathway can upregulate pathway-specific gene expression and are associated with clinical outcomes. Our study reveals the diverse mechanisms by which the mutational landscape of 5' UTRs can co-opt gene expression and demonstrates that single nucleotide alterations within 5' UTRs are functional in cancer.

DOI: https://doi.org/10.1038/s41467-021-24445-6
Nat Commun. 2021 07 09. 12(1): 4203

Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms in cardiomyocytes.

Chenchen Zhu, Jingyan Wu, Han Sun, Francesca Briganti, Benjamin Meder, Wu Wei, Lars M Steinmetz.

Alternative splicing generates differing RNA isoforms that govern phenotypic complexity of eukaryotes. Its malfunction underlies many diseases, including cancer and cardiovascular diseases. Comparative analysis of RNA isoforms at the genome-wide scale has been difficult. Here, we establish an experimental and computational pipeline that performs de novo transcript annotation and accurately quantifies transcript isoforms from cDNA sequences with a full-length isoform detection accuracy of 97.6%. We generate a searchable, quantitative human transcriptome annotation with 31,025 known and 5,740 novel transcript isoforms ( http://steinmetzlab.embl.de/iBrowser/ ). By analyzing the isoforms in the presence of RNA Binding Motif Protein 20 (RBM20) mutations associated with aggressive dilated cardiomyopathy (DCM), we identify 121 differentially expressed transcript isoforms in 107 cardiac genes. Our approach enables quantitative dissection of complex transcript architecture instead of mere identification of inclusion or exclusion of individual exons, as exemplified by the discovery of IMMT isoforms mis-spliced by RBM20 mutations. Thereby we achieve a path to direct differential expression testing independent of an existing annotation of transcript isoforms, providing more immediate biological interpretation and higher resolution transcriptome comparisons.

DOI: https://doi.org/10.1038/s41467-021-24484-z
Proc Natl Acad Sci U S A. 2021 Jul 20. pii: e2024562118. [Epub ahead of print]118(29):

MK2 degradation as a sensor of signal intensity that controls stress-induced cell fate.

Nuria Gutierrez-Prat, Monica Cubillos-Rojas, Begoña Cánovas, Antonija Kuzmanic, Jalaj Gupta, Ana Igea, Elisabet Llonch, Matthias Gaestel, Angel R Nebreda.

  Cell survival in response to stress is determined by the coordination of various signaling pathways. The kinase p38α is activated by many stresses, but the intensity and duration of the signal depends on the stimuli. How different p38α-activation dynamics may impact cell life/death decisions is unclear. Here, we show that the p38α-signaling output in response to stress is modulated by the expression levels of the downstream kinase MK2. We demonstrate that p38α forms a complex with MK2 in nonstimulated mammalian cells. Upon pathway activation, p38α phosphorylates MK2, the complex dissociates, and MK2 is degraded. Interestingly, transient p38α activation allows MK2 reexpression, reassembly of the p38α-MK2 complex, and cell survival. In contrast, sustained p38α activation induced by severe stress interferes with p38α-MK2 interaction, resulting in irreversible MK2 loss and cell death. MK2 degradation is mediated by the E3 ubiquitin ligase MDM2, and we identify four lysine residues in MK2 that are directly ubiquitinated by MDM2. Expression of an MK2 mutant that cannot be ubiquitinated by MDM2 enhances the survival of stressed cells. Our results indicate that MK2 reexpression and binding to p38α is critical for cell viability in response to stress and illustrate how particular p38α-activation patterns induced by different signals shape the stress-induced cell fate.

Keywords:  MDM2; MK2; cell survival; p38; stress

DOI:  https://doi.org/10.1073/pnas.2024562118
Nat Commun. 2021 07 09. 12(1): 4219

Improved CRISPR genome editing using small highly active and specific engineered RNA-guided nucleases.

Moritz J Schmidt, Ashish Gupta, Christien Bednarski, Stefanie Gehrig-Giannini, Florian Richter, Christian Pitzler, Michael Gamalinda, Christina Galonska, Ryo Takeuchi, Kui Wang, Caroline Reiss, Kerstin Dehne, Michael J Lukason, Akiko Noma, Cindy Park-Windhol, Mariacarmela Allocca, Albena Kantardzhieva, Shailendra Sane, Karolina Kosakowska, Brian Cafferty, Jan Tebbe, Sarah J Spencer, Scott Munzer, Christopher J Cheng, Abraham Scaria, Andrew M Scharenberg, André Cohnen, Wayne M Coco.

Streptococcus pyogenes (Spy) Cas9 has potential as a component of gene therapeutics for incurable diseases. One of its limitations is its large size, which impedes its formulation and delivery in therapeutic applications. Smaller Cas9s are an alternative, but lack robust activity or specificity and frequently recognize longer PAMs. Here, we investigated four uncharacterized, smaller Cas9s and found three employing a "GG" dinucleotide PAM similar to SpyCas9. Protein engineering generated synthetic RNA-guided nucleases (sRGNs) with editing efficiencies and specificities exceeding even SpyCas9 in vitro and in human cell lines on disease-relevant targets. sRGN mRNA lipid nanoparticles displayed manufacturing advantages and high in vivo editing efficiency in the mouse liver. Finally, sRGNs, but not SpyCas9, could be packaged into all-in-one AAV particles with a gRNA and effected robust in vivo editing of non-human primate (NHP) retina photoreceptors. Human gene therapy efforts are expected to benefit from these improved alternatives to existing CRISPR nucleases.

DOI: https://doi.org/10.1038/s41467-021-24454-5
Nat Commun. 2021 07 09. 12(1): 4202

Transcription coordinates histone amounts and genome content.

Kora-Lee Claude, Daniela Bureik, Dimitra Chatzitheodoridou, Petia Adarska, Abhyudai Singh, Kurt M Schmoller.

Biochemical reactions typically depend on the concentrations of the molecules involved, and cell survival therefore critically depends on the concentration of proteins. To maintain constant protein concentrations during cell growth, global mRNA and protein synthesis rates are tightly linked to cell volume. While such regulation is appropriate for most proteins, certain cellular structures do not scale with cell volume. The most striking example of this is the genomic DNA, which doubles during the cell cycle and increases with ploidy, but is independent of cell volume. Here, we show that the amount of histone proteins is coupled to the DNA content, even though mRNA and protein synthesis globally increase with cell volume. As a consequence, and in contrast to the global trend, histone concentrations decrease with cell volume but increase with ploidy. We find that this distinct coordination of histone homeostasis and genome content is already achieved at the transcript level, and is an intrinsic property of histone promoters that does not require direct feedback mechanisms. Mathematical modeling and histone promoter truncations reveal a simple and generalizable mechanism to control the cell volume- and ploidy-dependence of a given gene through the balance of the initiation and elongation rates.

DOI: https://doi.org/10.1038/s41467-021-24451-8
Mol Metab. 2021 Jul 10. pii: S2212-8778(21)00139-3. [Epub ahead of print] 101294

Physiological impact of in vivo stable isotope tracing on cancer metabolism.

Manuel Grima-Reyes, Adriana Martinez-Turtos, Ifat Abramovich, Eyal Gottlieb, Johanna Chiche, Jean-Ehrland Ricci.

  BACKGROUND: There is growing interest in the analysis of tumor metabolism to identify cancer-specific metabolic vulnerabilities and therapeutic targets. The identification of such candidate metabolic pathways mainly relies on the highly sensitive identification and quantitation of numerous metabolites and metabolic fluxes using metabolomics and isotope tracing analyses. However, nutritional requirements and metabolic routes used by cancer cells cultivated in vitro do not always reflect the metabolic demands of malignant cells within the tumor milieu. Therefore, to be able to understand how the metabolism of a tumor cell in its physiological environment differs from that of normal cells, these analyses must be performed in vivo.SCOPE OF REVIEW: This review covers the physiological impact of the exogenous administration of a stable isotope tracer into cancer animal models. We discuss specific aspects of in vivo isotope tracing protocols based on discrete bolus injections of a labeled metabolite: the tracer administration per se and the fasting period prior to tracer administration. In addition, we illustrate the complex physiological scenarios that arise when studying tumor metabolism by isotopic labeling in animal models fed with a diet restricted in a specific amino acid. Finally, we provide strategies to minimize those limitations.
MAJOR CONCLUSIONS: There is a growing evidence that metabolic dependencies in cancers are influenced by tissue environments, cancer lineage, and genetic events. More and more studies are describing discrepancies in tumor metabolic dependencies when studied in in vitro settings or in in vivo models, including cancer patients. Therefore, in depth in vivo profiling of tumor metabolic routes within the appropriate patho-physiological environment will be key to identifying relevant alterations that contribute to cancer onset and progression.

Keywords:  Fasting; Inter-organ exchange; Stable isotope tracing; Tracer administration; Tumor metabolism

DOI:  https://doi.org/10.1016/j.molmet.2021.101294
Elife. 2021 Jul 12. pii: e67753. [Epub ahead of print]10

E2F/Dp inactivation in fat body cells triggers systemic metabolic changes.

Maria Paula Zappia, Ana Guarner, Nadia Kellie-Smith, Alice Rogers, Robert Morris, Brandon Nicolay, Myriam Boukhali, Wilhelm Haas, Nicholas Dyson, Maxim V Frolov.

  The E2F transcription factors play a critical role in controlling cell fate. In Drosophila, the inactivation of E2F in either muscle or fat body results in lethality, suggesting an essential function for E2F in these tissues. However, the cellular and organismal consequences of inactivating E2F in these tissues are not fully understood. Here, we show that the E2F loss exerts both tissue-intrinsic and systemic effects. The proteomic profiling of E2F-deficient muscle and fat body revealed that E2F regulates carbohydrate metabolism, a conclusion further supported by metabolomic profiling. Intriguingly, animals with E2F-deficient fat body had a lower level of circulating trehalose and reduced storage of fat. Strikingly, a sugar supplement was sufficient to restore both trehalose and fat levels, and subsequently, rescued animal lethality. Collectively, our data highlight the unexpected complexity of E2F mutant phenotype, which is a result of combining both tissue-specific and systemic changes that contribute to animal development.

Keywords:  D. melanogaster; cancer biology; developmental biology

DOI:  https://doi.org/10.7554/eLife.67753
JCI Insight. 2021 Jul 13. pii: 147096. [Epub ahead of print]

Inhibition of mTOR signaling and clinical activity of metformin in oral premalignant lesions.

J Silvio Gutkind, Alfredo Molinolo, Xingyu Wu, Zhiyong Wang, Daniela Nachmanson, Olivier Harismendy, Ludmil B Alexandrov, Beverly R Wuertz, Frank G Ondrey, Denise M Laronde, Leigha D Rock, Miriam P Rosin, Charles S Coffey, Valerie D Butler, Lisa Bengtson, Chiu-Hsieh Hsu, Julie E Bauman, Stephen M Hewitt, Ezra Ew Cohen, H H Sherry Chow, Scott M Lippman, Eva Szabo.

  BACKGROUND: The aberrant activation of the PI3K/mTOR signaling circuitry is one of the most frequently dysregulated signaling events in head and neck squamous cell carcinoma (HNSCC). Here, we conducted a single-arm, open label phase IIa clinical trial (NCT02581137) in individuals with oral premalignant lesions (OPL) to explore the potential of metformin to target PI3K/mTOR signaling for HNSCC prevention.METHODS: Subjects with OPL, otherwise healthy and without diabetes, underwent pre- and post-treatment clinical exam and biopsy. Participants received metformin for 12 weeks (week 1, 500 mg; week 2, 1,000 mg; week 3-12, 2,000 mg daily). Pre- and post-treatment biopsies, saliva, and blood were obtained for biomarker analysis, including immunohistochemical (IHC) assessment of mTOR signaling and exome sequencing.
RESULTS: Twenty-three participants were evaluable for response. The clinical response rate (defined as ≥50% reduction in lesion size) was 17%. While lower than the proposed threshold for favorable clinical response, the histologic response rate (improvement in histologic grade) was 60%, including 17% complete responses and 43% partial responses. Logistic regression analysis revealed that when compared to never smokers, current and former smokers had statistically significantly increased histologic responses (p=0.016). Remarkably, a significant correlation existed between decreased mTOR activity (pS6 IHC staining) in the basal epithelial layer of OPL and the histological (p=0.04) and clinical (p=0.01) responses.
CONCLUSIONS: This is the first phase II trial of metformin in individuals with OPL, providing evidence that metformin administration results in encouraging histological responses and mTOR pathway modulation, thus supporting its further investigation as a chemopreventive agent.

Keywords:  Clinical Trials; Head and neck cancer; Signal transduction

DOI:  https://doi.org/10.1172/jci.insight.147096
Mol Cell Biochem. 2021 Jul 10.

Role of PI3K/Akt signaling pathway in cardiac fibrosis.

Wuming Qin, Linghui Cao, Isaac Yaw Massey.

  Heart failure (HF) is considered as a severe health problem worldwide, while cardiac fibrosis is one of the main driving factors for the progress of HF. Cardiac fibrosis was characterized by changes in cardiomyocytes, cardiac fibroblasts, ratio of collagen (COL) I/III, and the excessive production and deposition of extracellular matrix (ECM), thus forming a scar tissue, which leads to pathological process of cardiac structural changes and systolic as well as diastolic dysfunction. Cardiac fibrosis is a common pathological change of many advanced cardiovascular diseases including ischemic heart disease, hypertension, and HF. Accumulated studies have proven that phosphoinositol-3 kinase (PI3K)/Akt signaling pathway is involved in regulating the occurrence, progression and pathological formation of cardiac fibrosis via regulating cell survival, apoptosis, growth, cardiac contractility and even the transcription of related genes through a series of molecules including mammalian target of rapamycin (mTOR), glycogen synthase kinase 3 (GSK-3), forkhead box proteins O1/3 (FoxO1/3), and nitric oxide synthase (NOS). Thus, the review focuses on the role of PI3K/Akt signaling pathway in the cardiac fibrosis. The information reviewed here should be significant in understanding the role of PI3K/Akt in cardiac fibrosis and contribute to the design of further studies related to PI3K/Akt and the cardiac fibrotic response, as well as sought to shed light on a potential treatment for cardiac fibrosis.

Keywords:  Cardiac fibrosis; PI3K/Akt signaling pathway

DOI:  https://doi.org/10.1007/s11010-021-04219-w
Aging Cell. 2021 Jul 11. e13432

FoxO3 deficiency in cortical astrocytes leads to impaired lipid metabolism and aggravated amyloid pathology.

Shuqi Du, Feng Jin, Laure Maneix, Manasee Gedam, Yin Xu, Andre Catic, Meng C Wang, Hui Zheng.

  The rise of life expectancy of the human population is accompanied by the drastic increases of age-associated diseases, in particular Alzheimer's disease (AD), and underscores the need to understand how aging influences AD development. The Forkhead box O transcription factor 3 (FoxO3) is known to mediate aging and longevity downstream of insulin/insulin-like growth factor signaling across species. However, its function in the adult brain under physiological and pathological conditions is less understood. Here, we report a region and cell-type-specific regulation of FoxO3 in the central nervous system (CNS). We found that FoxO3 protein levels were reduced in the cortex, but not hippocampus, of aged mice. FoxO3 was responsive to insulin/AKT signaling in astrocytes, but not neurons. Using CNS Foxo3-deficient mice, we reveal that loss of FoxO3 led to cortical astrogliosis and altered lipid metabolism. This is associated with impaired metabolic homoeostasis and β-amyloid (Aβ) uptake in primary astrocyte cultures. These phenotypes can be reversed by expressing a constitutively active FOXO3 but not a FOXO3 mutant lacking the transactivation domain. Loss of FoxO3 in 5xFAD mice led to exacerbated Aβ pathology and synapse loss and altered local response of astrocytes and microglia in the vicinity of Aβ plaques. Astrocyte-specific overexpression of FOXO3 displayed opposite effects, suggesting that FoxO3 functions cell autonomously to mediate astrocyte activity and also interacts with microglia to address Aβ pathology. Our studies support a protective role of astroglial FoxO3 against brain aging and AD.

Keywords:  Alzheimer's disease; FoxO3; aging; astrocytes; mice; β-amyloid

DOI:  https://doi.org/10.1111/acel.13432
Sci Rep. 2021 Jul 12. 11(1): 14291

Mitofusion is required for MOTS-c induced GLUT4 translocation.

Khushwant S Bhullar, Nan Shang, Evan Kerek, Kaiyu Wu, Jianping Wu.

MOTS-c (mitochondrial ORF of the twelve S-c) is a 16-amino-acid mitochondrial peptide that has been shown to counter insulin resistance and alleviate obesity in vivo. However, the mechanisms involved in the pharmacological action of MOTS-c remain elusive. Based on the ability of MOTS-c to improve insulin resistance and promote cold adaptation, we hypothesized that MOTS-c might play a role in boosting the number of mitochondria in a cell. We found that treatment of mammalian cells with MOTS-c increased protein levels of TFAM, COX4, and NRF1, which are markers for mitochondrial biogenesis. However, flow cytometry analysis using MitoTracker Green revealed a sharp reduction in the mitochondrial count after MOTS-c treatment. We then anticipated possible synchronized activation of mitofusion/mitochondrial fusion by MOTS-c following the onset of mitochondrial biogenesis. This was confirmed after a significant increase in protein levels two GTPases, OPA1, and MFN2, both vital for the fusion of mammalian mitochondria. Finally, we found that inhibition of the two GTPases by TNFα abrogated the ability of MOTS-c to prompt GLUT4 translocation and glucose uptake. Similar results were obtained by siRNA KD of MFN2 as well. Our results reveal for the first time a pathway that links mitofusion to MOTS-c-induced GLUT4 translocation.

DOI: https://doi.org/10.1038/s41598-021-93735-2